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Hi there, I'm a member of the team at Google responsible for this dataset. I don't see an artfact at exactly those coordinates, but is this nearby location wha

Hi there, I'm a member of the team at Google responsible for this dataset. I don't see an artfact at exactly those coordinates, but is this nearby location what you are referring to: tinyurl.com/4rpas73s That appears to be a knife mark. This dataset was assembled from over 5000 tissue sections each cut at a thickness of just 30 nanometers using a device called an ultramicrotome. Tiny imperfections can develop in the diamond knife used by the ultramicrotome, which unfortunately can result in artifacts like that. Fortunately such artifacts are unlikely to affect the same location on multiple consecutive sections, and our segmentation algorithms are robust enough to segment through those locations. By the way, one cool thing about the viewer, neuroglancer, is that you can just copy the URL to link directly to any particular view.

akiselev 5y ago
Was this done using the knife edge microscopy technique or was each tissue sliced imaged after mechanically separating it from the rest?
- mjanusz 5y ago
  The latter. The tissue block is sliced first in the ATUM which collects the sections on tape. These are then mounted on silicon wafers, and imaged with the MultiSEM. Our preprint at https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1 https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1 has some more details about the process, including figures illustrating the ATUM and the tissue block. (I'm one of the authors of the paper)
- jeremybms 5y ago
  This dataset was collected using physical ~33nm-thick sections that were cut with a diamond knife and stored (and preserved) on a carbon tape before imaging with a multi-beam scanning electron microscope. You can get the full details in the preprint paper: https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1 https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1
nynx 5y ago
Fascinating work. Does your personal interest in this some from the perspective of (mid/long-term future) WBE?
elteto 5y ago
Hi Jeremy! Thanks for responding, yes that is exactly what I was referring to (I must have mistyped the coordinates). I didn't copy the URL initially because it is rather long... I should have used tinyurl like you did.

akiselev 5y ago

Was this done using the knife edge microscopy technique or was each tissue sliced imaged after mechanically separating it from the rest?

mjanusz 5y ago
The latter. The tissue block is sliced first in the ATUM which collects the sections on tape. These are then mounted on silicon wafers, and imaged with the MultiSEM. Our preprint at https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1 https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1 has some more details about the process, including figures illustrating the ATUM and the tissue block. (I'm one of the authors of the paper)
jeremybms 5y ago
This dataset was collected using physical ~33nm-thick sections that were cut with a diamond knife and stored (and preserved) on a carbon tape before imaging with a multi-beam scanning electron microscope. You can get the full details in the preprint paper: https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1 https://www.biorxiv.org/content/10.1101/2021.05.29.446289v1

nynx 5y ago

Fascinating work. Does your personal interest in this some from the perspective of (mid/long-term future) WBE?

elteto 5y ago

Hi Jeremy! Thanks for responding, yes that is exactly what I was referring to (I must have mistyped the coordinates). I didn't copy the URL initially because it is rather long... I should have used tinyurl like you did.